You shouldn't have to do this anymore with Perl for Windows, as it automatically updates the Registry, so as long as you name your files with an appropriate extension - .pl or maybe .cgi then Windows should automatically detect these as Perl scripts and just treat your shebang line as a comment.

Update: You might also have to uncomment the following line in your httpd.conf file to ensure that Apache looks up the correct location within the Windows Registry rather than refering to the shebang line.